Th passkey is stored on the client and matched with valid passkeys. It is stored in config.xml for the v7 client, and in a small sql database for the v8 client which is what it appears you are using based on finding /var/lib/fah-client instead of /var/lib/fahclient.I entered a passkey when I first started folding. Is it possible that the server lost it?
First you need to figure out why your machines are not completing WUs before the deadlines. Then I would recommend requesting a new passkey by using a different username or email address. It will send the same passkey if you fill out the request form with the same name and email. Then it will take completing 10 WUs before you will start getting bonus points again.